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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $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
$disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ) $local_species = 'ach' $disabled = '' $selected = '' $num_hits = (int) 0
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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ) $local_species = 'lja' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ), 'gf_id' => 'HOM05D001385', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001385' ), 'data_identifier' => 'HOM05D001385', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001385', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '453', 'num_species' => '96' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A04p01750' => 'bna', 'A07p25030' => 'bna', 'A09p52520' => 'bna', 'Aa31LG11G6280' => 'aar', 'Aa31LG3G4200' => 'aar', 'Aa31LG9G15170' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2927' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_362.1920' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.2342' => 'aag', 'Actinidia03412' => 'ach', 'Actinidia05783' => 'ach', 'Actinidia10868' => 'ach', 'Actinidia12635' => 'ach', 'Actinidia30946' => 'ach', 'Actinidia31488' => 'ach', 'Ah.01g010370' => 'amhyb', 'Ah.01g010380' => 'amhyb', 'Ah.02g117390' => 'amhyb', 'Ah.02g117400' => 'amhyb', 'Ah.02g117910' => 'amhyb', 'Ah.02g120850' => 'amhyb', 'Ah.02g120890' => 'amhyb', 'Ah.02g120900' => 'amhyb', 'Ah.02g121100' => 'amhyb', 'Ah.02g123480' => 'amhyb', 'Ah.05g175550' => 'amhyb', 'Ah.05g177710' => 'amhyb', 'Ah.05g177810' => 'amhyb', 'Ah.06g185530' => 'amhyb', 'Ah.07g199140' => 'amhyb', 'Ah.08g221340' => 'amhyb', 'Ah.10g025260' => 'amhyb', 'Ah.10g025350' => 'amhyb', 'Ah.10g025640' => 'amhyb', 'Ah.13g066910' => 'amhyb', 'AL3G22490' => 'aly', 'AL5G42460' => 'aly', 'AL6G15190' => 'aly', 'Aqoxy1G03178' => 'aox', 'Aqoxy3G02581' => 'aox', 'Aqoxy3G02871' => 'aox', 'Aqoxy6G02065' => 'aox', 'arahy.Tifrunner.gnm1.ann1.17QRGR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6PAV3F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6S7C55' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GZ87H9' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K7HT3I' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N075P8' => 'arhy', 'AT3G10950' => 'ath', 'AT3G60245' => 'ath', 'ATR0665G487' => 'atr', 'ATR1098G129' => 'atr', 'AUR62002714' => 'cqu', 'AUR62002718' => 'cqu', 'AUR62002875' => 'cqu', 'AUR62005473' => 'cqu', 'AUR62005475' => 'cqu', 'AUR62010149' => 'cqu', 'AUR62013145' => 'cqu', 'AUR62013585' => 'cqu', 'AUR62013775' => 'cqu', 'AUR62013950' => 'cqu', 'AUR62014303' => 'cqu', 'AUR62016349' => 'cqu', 'AUR62017452' => 'cqu', 'AUR62019603' => 'cqu', 'AUR62020405' => 'cqu', 'AUR62023381' => 'cqu', 'AUR62026509' => 'cqu', 'AUR62026964' => 'cqu', 'AUR62027999' => 'cqu', 'AUR62028251' => 'cqu', 'AUR62028470' => 'cqu', 'AUR62029692' => 'cqu', 'AUR62030226' => 'cqu', 'AUR62033102' => 'cqu', 'AUR62034140' => 'cqu', 'AUR62034205' => 'cqu', 'AUR62034385' => 'cqu', 'AUR62034766' => 'cqu', 'AUR62035309' => 'cqu', 'AUR62036601' => 'cqu', 'AUR62036605' => 'cqu', 'AUR62036620' => 'cqu', 'AUR62037120' => 'cqu', 'AUR62037359' => 'cqu', 'AUR62037756' => 'cqu', 'AUR62037924' => 'cqu', 'AUR62037931' => 'cqu', 'AUR62038951' => 'cqu', 'AUR62039729' => 'cqu', 'AUR62040023' => 'cqu', 'AUR62040137' => 'cqu', 'AUR62040146' => 'cqu', 'AUR62040186' => 'cqu', 'AUR62040865' => 'cqu', 'AUR62041069' => 'cqu', 'AUR62041104' => 'cqu', 'AUR62041185' => 'cqu', 'AUR62041856' => 'cqu', 'AUR62041907' => 'cqu', 'AUR62042068' => 'cqu', 'AUR62042499' => 'cqu', 'AUR62042540' => 'cqu', 'AUR62042649' => 'cqu', 'AUR62042768' => 'cqu', 'AUR62042851' => 'cqu', 'AUR62042852' => 'cqu', 'AUR62042914' => 'cqu', 'AUR62043185' => 'cqu', 'AUR62043334' => 'cqu', 'AUR62043689' => 'cqu', 'AUR62043798' => 'cqu', 'AUR62043841' => 'cqu', 'AUR62044135' => 'cqu', 'AUR62044406' => 'cqu', 'AUR62044453' => 'cqu', 'AUR62044701' => 'cqu', 'BcaB02g07425' => 'bca', 'BcaB02g08183' => 'bca', 'BcaC02g10141' => 'bca', 'BcaC07g40419' => 'bca', 'BcaC08g45043' => 'bca', 'BcaNung07144' => 'bca', 'BolC4t24788H' => 'bol', 'BolC6t37825H' => 'bol', 'BraA07t30143Z' => 'bra', 'BraA09t40683Z' => 'bra', 'C04p32400' => 'bna', 'C06p26640' => 'bna', 'C08p35280' => 'bna', 'CAN.G756.28' => 'can', 'CAN.G845.26' => 'can', 'CANSAT21G2590' => 'cansat', 'CANSAT25G2455' => 'cansat', 'CARHR085530' => 'chi', 'CARHR129340' => 'chi', 'CARHR170560' => 'chi', 'Carub.0003s1022' => 'cru', 'Carub.0004s1687' => 'cru', 'Carub.0005s2699' => 'cru', 'Ca_22026_v3' => 'car', 'Ca_22050_v3' => 'car', 'Ca_23638_v3' => 'car', 'Ca_24619_v3' => 'car', 'CBR_g25964' => 'cbr', 'Cc02_g25460' => 'ccan', 'Cc08_g01480' => 'ccan', 'CDE02G4742' => 'cde', 'CDE05G0172' => 'cde', 'CDE05G2975' => 'cde', 'Cfa010935' => 'cfa', 'Cfa012352' => 'cfa', 'Cfa015174' => 'cfa', 'Ciclev10006403m.g' => 'ccl', 'Ciclev10022898m.g' => 'ccl', 'Ciclev10023068m.g' => 'ccl', 'Ciclev10024386m.g' => 'ccl', 'Ciclev10029778m.g' => 'ccl', 'CiPaw.01G101600' => 'cil', 'CiPaw.03G079400' => 'cil', 'CiPaw.12G056500' => 'cil', 'CiPaw.13G022900' => 'cil', 'CiPaw.14G017700' => 'cil', 'ClCG05G002990' => 'cla', 'ClCG06G008110' => 'cla', 'ClCG09G012610' => 'cla', 'COL.COLO4_06697' => 'col', 'COL.COLO4_12364' => 'col', 'Cpa.g.c28699.3' => 'cpa', 'Cpa.g.sc98.60' => 'cpa', 'Cre06.g257150' => 'cre', 'CsaV3_2G011060' => 'csa', 'CsaV3_3G010610' => 'csa', 'CSS0032979' => 'camsi', 'CSS0035818' => 'camsi', 'DCAR_005593' => 'dca', 'DCAR_008316' => 'dca', 'DCAR_015796' => 'dca', 'DCAR_017294' => 'dca', 'DCAR_025038' => 'dca', 'Dinv25156' => 'din', 'Dinv43596' => 'din', 'Dinv44035' => 'din', 'Duzib068G0916' => 'dzi', 'Duzib084G0554' => 'dzi', 'Duzib133G0721' => 'dzi', 'Duzib138G1729' => 'dzi', 'Duzib205G0911' => 'dzi', 'ECA233G5964' => 'eca', 'ECA234G0989' => 'eca', 'ECA240G1672' => 'eca', 'ECA246G3291' => 'eca', 'EL10Ac1g00730' => 'bvu', 'EL10Ac1g01131' => 'bvu', 'EL10Ac1g01188' => 'bvu', 'EL10Ac1g01824' => 'bvu', 'EL10Ac1g02023' => 'bvu', 'EL10Ac1g02060' => 'bvu', 'EL10Ac2g03907' => 'bvu', 'EL10Ac3g06245' => 'bvu', 'EL10Ac3g06349' => 'bvu', 'EL10Ac3g06415' => 'bvu', 'EL10Ac4g08702' => 'bvu', 'EL10Ac4g08867' => 'bvu', 'EL10Ac4g08894' => 'bvu', 'EL10Ac4g08959' => 'bvu', 'EL10Ac4g09023' => 'bvu', 'EL10Ac5g11862' => 'bvu', 'EL10Ac6g14099' => 'bvu', 'EL10Ac6g14392' => 'bvu', 'EL10Ac6g14499' => 'bvu', 'EL10Ac6g14698' => 'bvu', 'EL10Ac7g16607' => 'bvu', 'EL10Ac7g17544' => 'bvu', 'EL10Ac7g18151' => 'bvu', 'EL10Ac8g19533' => 'bvu', 'EL10Ac8g19748' => 'bvu', 'EL10Ac8g19807' => 'bvu', 'EL10Ac9g20863' => 'bvu', 'EL10Ac9g20910' => 'bvu', 'EL10Ac9g21092' => 'bvu', 'EL10Ac9g21493' => 'bvu', 'EL10As26g24239' => 'bvu', 'EL10As2g23275' => 'bvu', 'Eucgr.B02533' => 'egr', 'Eucgr.E00333' => 'egr', 'Eucgr.L01912' => 'egr', 'FAN01G1953' => 'fan', 'FAN03G1596' => 'fan', 'FAN04G1054' => 'fan', 'FAN06G4616' => 'fan', 'FAN08G0965' => 'fan', 'FAN10G0963' => 'fan', 'FAN10G4114' => 'fan', 'FAN13G0799' => 'fan', 'FAN18G3150' => 'fan', 'FvH4_5g20720' => 'fve', 'FvH4_5g33510' => 'fve', 'FvH4_7g09070' => 'fve', 'Glyma.01G203600' => 'gma', 'Glyma.03G107000' => 'gma', 'Glyma.05G067400' => 'gma', 'Glyma.07G118600' => 'gma', 'Glyma.11G039200' => 'gma', 'Glyma.17G149600' => 'gma', 'Gohir.A06G063500' => 'ghi', 'Gohir.A08G140200' => 'ghi', 'Gohir.A08G161900' => 'ghi', 'Gohir.A09G197500' => 'ghi', 'Gohir.A12G212200' => 'ghi', 'Gohir.D06G062201' => 'ghi', 'Gohir.D08G161200' => 'ghi', 'Gohir.D08G181900' => 'ghi', 'Gohir.D09G192100' => 'ghi', 'Gohir.D12G214700' => 'ghi', 'Gorai.004G167500' => 'gra', 'Gorai.004G190800' => 'gra', 'Gorai.006G214900' => 'gra', 'Gorai.008G230300' => 'gra', 'Gorai.010G072500' => 'gra', 'GSVIVG01013278001' => 'vvi', 'GSVIVG01018328001' => 'vvi', 'HanXRQChr03g0089601' => 'han', 'HanXRQChr06g0167161' => 'han', 'HanXRQChr13g0419171' => 'han', 'HanXRQChr16g0520981' => 'han', 'Haze_02891' => 'cav', 'Haze_08344' => 'cav', 'Hma1.2p1_1672F.1_g296840' => 'hma', 'Hma1.2p1_1673F.1_g296910' => 'hma', 'HPP92_006327' => 'vpl', 'HPP92_024171' => 'vpl', 'HPP92_027878' => 'vpl', 'Hund00070' => 'sun', 'Hund06374' => 'sun', 'Hund06375' => 'sun', 'Hund07622' => 'sun', 'Hund17118' => 'sun', 'Hund20142' => 'sun', 'Hund22136' => 'sun', 'Hund24609' => 'sun', 'Hund27416' => 'sun', 'Lalb_Chr05g0214181' => 'lal', 'Lalb_Chr05g0220841' => 'lal', 'Lalb_Chr09g0324061' => 'lal', 'Lalb_Chr09g0329741' => 'lal', 'Lalb_Chr12g0210401' => 'lal', 'Lalb_Chr16g0379321' => 'lal', 'Lalb_Chr16g0386361' => 'lal', 'Lj3g0027855' => 'lja', 'Lj4g0019443' => 'lja', 'Lsat_1_v5_gn_4_38201' => 'lsa', 'Lsat_1_v5_gn_6_94921' => 'lsa', 'Lsat_1_v5_gn_9_68301' => 'lsa', 'Manes.05G057400' => 'mes', 'Manes.15G170900' => 'mes', 'Manes.17G022800' => 'mes', 'Mapoly0053s0100' => 'mpo', 'Mapoly0086s0038' => 'mpo', 'Mapoly0095s0001' => 'mpo', 'MBI04_g20751_MAGBIO' => 'mbi', 'MBI12_g21989_MAGBIO' => 'mbi', 'MBI16_g24684_MAGBIO' => 'mbi', 'MBI17_g39742_MAGBIO' => 'mbi', 'MBI17_g40224_MAGBIO' => 'mbi', 'MBI18_g13697_MAGBIO' => 'mbi', 'MCO06G200' => 'mco', 'MD02G1221600' => 'mdo', 'MD04G1053900' => 'mdo', 'MD06G1044600' => 'mdo', 'MD07G1094700' => 'mdo', 'MD13G1011900' => 'mdo', 'Medtr0199s0040' => 'mtr', 'Medtr4g099160' => 'mtr', 'Medtr4g103340' => 'mtr', 'Medtr8g007485' => 'mtr', 'MELO3C003342.2' => 'cme', 'MELO3C006280.2' => 'cme', 'MELO3C020369.2' => 'cme', 'Migut.B01500' => 'egut', 'Migut.N01721' => 'egut', 'MSTRG.20667' => 'ama', 'MSTRG.28137' => 'ama', 'Nitab4.5_0000057g0090' => 'nta', 'Nitab4.5_0000185g0260' => 'nta', 'Nitab4.5_0000293g0100' => 'nta', 'Nitab4.5_0000506g0210' => 'nta', 'Nitab4.5_0000563g0070' => 'nta', 'Nitab4.5_0000590g0030' => 'nta', 'Nitab4.5_0002341g0010' => 'nta', 'Nitab4.5_0002668g0060' => 'nta', 'Nitab4.5_0006060g0010' => 'nta', 'Nitab4.5_0008425g0020' => 'nta', 'Nitab4.5_0011026g0010' => 'nta', 'Nitab4.5_0013289g0010' => 'nta', 'Nn1g00725' => 'nnu', 'Nn1g09861' => 'nnu', 'Oeu012024.2' => 'oeu', 'Oeu024397.1' => 'oeu', 'Oeu034851.1' => 'oeu', 'Os01g0679700' => 'osa', 'Os05g0557000' => 'osa', 'Peaxi162Scf00023g00419' => 'pax', 'Peaxi162Scf00102g00733' => 'pax', 'Peaxi162Scf00103g01212' => 'pax', 'Peaxi162Scf00190g00610' => 'pax', 'Peaxi162Scf00198g01030' => 'pax', 'Peaxi162Scf00715g00114' => 'pax', 'Peaxi162Scf00793g00337' => 'pax', 'Peaxi162Scf00903g00005' => 'pax', 'PGR031G1362' => 'pgr', 'PGR031G2214' => 'pgr', 'PGSC0003DMG400001690' => 'stu', 'PGSC0003DMG400001849' => 'stu', 'PGSC0003DMG400013127' => 'stu', 'PGSC0003DMG401020509' => 'stu', 'Phvul.003G226400' => 'pvu', 'Phvul.010G044100' => 'pvu', 'Potri.001G149300' => 'ptr', 'Potri.002G140100' => 'ptr', 'Potri.003G085100' => 'ptr', 'Potri.014G052400' => 'ptr', 'Pp3c11_2550' => 'ppa', 'Pp3c1_1530' => 'ppa', 'Pp3c26_15390' => 'ppa', 'Pp3c2_34770' => 'ppa', 'Pp3c3_1620' => 'ppa', 'Pp3c6_19330' => 'ppa', 'Pp3c7_21150' => 'ppa', 'PRCOL_00005654' => 'pco', 'Prupe.2G119100' => 'ppe', 'Prupe.5G052800' => 'ppe', 'Psat2g175400' => 'psa', 'Psat4g076440' => 'psa', 'Psat4g222680' => 'psa', 'PSO063G1321' => 'pso', 'PSO135G0079' => 'pso', 'PSO384G1218' => 'pso', 'PSO675G3977' => 'pso', 'PSO732G0559' => 'pso', 'PSO732G0618' => 'pso', 'PSO782G0348' => 'pso', 'QL04p026571' => 'qlo', 'QL04p026974' => 'qlo', 'QL12p008409' => 'qlo', 'RcHm_v2.0_Chr1g0344921' => 'rch', 'RcHm_v2.0_Chr3g0477031' => 'rch', 'RcHm_v2.0_Chr7g0206491' => 'rch', 'Rhsim07G0038500' => 'rsi', 'Sabra02G0109400' => 'sbr', 'Sabra03G0055200' => 'sbr', 'Sabra14G0037200' => 'sbr', 'Sabra14G0039300' => 'sbr', 'SalBow4G0790' => 'sbo', 'SalBow7G4814' => 'sbo', 'Sc02g0003220' => 'sci', 'Sc03g0005880' => 'sci', 'Sc08g0003950' => 'sci', 'Sc08g0003960' => 'sci', 'Sc10g0006250' => 'sci', 'Sc11g0008180' => 'sci', 'Sc11g0008190' => 'sci', 'Sc13g0007340' => 'sci', 'Sc26g0001700' => 'sci', 'Sed0000374' => 'sed', 'Sed0001002' => 'sed', 'Sed0012252' => 'sed', 'Sed0020270' => 'sed', 'SEGI_22881' => 'sgi', 'SGA_v2.0_scaffold52G19260' => 'sas', 'SGA_v2.0_scaffold95G28718' => 'sas', 'SMO367G0710' => 'smo', 'Solyc08g007140.4' => 'sly', 'Solyc08g077710.3' => 'sly', 'Solyc08g077720.3' => 'sly', 'Solyc10g061970.2' => 'sly', 'Sopen08g003090' => 'spe', 'Sopen08g026220' => 'spe', 'Sopen08g026230' => 'spe', 'Sopen10g026220' => 'spe', 'Sp3g09280' => 'spa', 'Sp5g02960' => 'spa', 'TAR374G0227' => 'tar', 'TAR624G0086' => 'tar', 'TAR628G0938' => 'tar', 'TAR629G3316' => 'tar', 'TAR633G0843' => 'tar', 'TAR636G0128' => 'tar', 'THA.LOC104807942' => 'tha', 'THA.LOC104812739' => 'tha', 'THA.LOC104814455' => 'tha', 'THA.LOC104817183' => 'tha', 'Thecc.01G401200' => 'tca', 'Thecc.03G237500' => 'tca', 'Thhalv10006337m.g' => 'esa', 'Thhalv10017838m.g' => 'esa', 'Thhalv10021837m.g' => 'esa', 'TPR.G17122' => 'tpr', 'TPR.G19190' => 'tpr', 'TPR.G22967' => 'tpr', 'TWI14G0404' => 'twi', 'TWI23G0945' => 'twi', 'TWI59G0979' => 'twi', 'unitig_0.g84' => 'ugi', 'unitig_60.g25453' => 'ugi', 'vmacro00379' => 'vma', 'vmacro13527' => 'vma', 'vmacro14119' => 'vma', 'Zm00001eb085730' => 'zma', 'Zm00001eb207840' => 'zma', 'Zm00001eb232530' => 'zma', 'Zm00001eb343250' => 'zma' ) $gf_id = 'HOM05D001385' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001385' ) $data_identifier = 'HOM05D001385' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 6, 'aar' => (int) 3, 'aag' => (int) 3, 'ach' => (int) 6, 'amhyb' => (int) 20, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 6, 'ath' => (int) 2, 'atr' => (int) 2, 'cqu' => (int) 66, 'bca' => (int) 6, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 3, 'cru' => (int) 3, 'car' => (int) 4, 'cbr' => (int) 1, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 3, 'ccl' => (int) 5, 'cil' => (int) 5, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 2, 'dca' => (int) 5, 'din' => (int) 3, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 32, 'egr' => (int) 3, 'fan' => (int) 9, 'fve' => (int) 3, 'gma' => (int) 6, 'ghi' => (int) 10, 'gra' => (int) 5, 'vvi' => (int) 2, 'han' => (int) 4, 'cav' => (int) 2, 'hma' => (int) 2, 'vpl' => (int) 3, 'sun' => (int) 9, 'lal' => (int) 7, 'lja' => (int) 2, 'lsa' => (int) 3, 'mes' => (int) 3, 'mpo' => (int) 3, 'mbi' => (int) 6, 'mco' => (int) 1, 'mdo' => (int) 5, 'mtr' => (int) 4, 'cme' => (int) 3, 'egut' => (int) 2, 'ama' => (int) 2, 'nta' => (int) 12, 'nnu' => (int) 2, 'oeu' => (int) 3, 'osa' => (int) 2, 'pax' => (int) 8, 'pgr' => (int) 2, 'stu' => (int) 4, 'pvu' => (int) 2, 'ptr' => (int) 4, 'ppa' => (int) 7, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 7, 'qlo' => (int) 3, 'rch' => (int) 3, 'rsi' => (int) 1, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 9, 'sed' => (int) 4, 'sgi' => (int) 1, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 2, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 2, 'esa' => (int) 3, 'tpr' => (int) 3, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 3, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb343250' $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